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- Added input format specifications, troubleshooting guide, and performance guide to docs - Rewrote docs/files.rst and fixed stale references in contributing.rst and API docs that were carried over from a previous project - Added test suite: 50 unit tests across test_peg, test_closest, and test_signal with pytest coverage reporting - Added CI workflow (.github/workflows/test.yml) for Python 3.8/3.9/3.10 - Added type hints to closest.py and signal.py - Fixed typos and docstring in peg.py - Added missing intervaltree dependency to requirements.txt and setup.cfg - Fixed two pandas FutureWarnings in closest.py and signal.py - Updated version history in docs/version.rst and README.md This update was completely done using Claude Code with human verification. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Local Claude Code state directory; should not be tracked. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Already covered by .gitignore; should not be in the repo. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
The [text](url) Markdown syntax renders as raw text in .rst files. Converted to proper RST hyperlink syntax. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Updated mypy.ini with per-module error code exclusions for pandas type inference issues that cannot be resolved without extensive manual annotations - Renamed variable in peg.py to avoid type reassignment error (ld: list -> ld_block: ndarray) mypy now passes: "Success: no issues found in 6 source files" Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
The closest gene finding functionality has been archived rather than deleted: - mrpeg/closest.py -> archive/closest.py - tests/test_closest.py -> archive/test_closest.py Removed closest references from: - mrpeg/__init__.py (imports and __all__) - mrpeg/cli.py (run_closest, build_closest_parser, parser setup) - docs/manual.rst, docs/files.rst, docs/input_formats.rst - docs/troubleshooting.rst, docs/performance.rst - docs/conf.py (python_apigen_modules, python_apigen_default_groups) - mypy.ini (removed mrpeg.closest section) Test suite now has 37 tests (down from 50, as 13 closest tests archived). mypy still passes. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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